Align The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized)
to candidate 353168 BT3642 Na+-dependent transporter (NCBI ptt file)
Query= TCDB::Q8RHM5 (438 letters) >FitnessBrowser__Btheta:353168 Length = 456 Score = 209 bits (532), Expect = 1e-58 Identities = 147/456 (32%), Positives = 235/456 (51%), Gaps = 40/456 (8%) Query: 8 FQSKIGFILTCVGSAVGMANIWAFPYRVGKYGGAVFLLIYFMFIALFSYVGLSAEYLIGR 67 F SK+G IL GSAVG+ NIW FPY G +GGA F+LIY + L L AE+LIGR Sbjct: 9 FGSKLGVILASAGSAVGLGNIWRFPYETGNHGGAAFILIYLGCVFLLGLPILIAEFLIGR 68 Query: 68 RAETGTLGSYEYA-----WKDVGKGKLGYGLAYIPLLGSMSIAIGYAVIAAWVLRTFGAA 122 R+ T G+Y+ W+ VG+ + +L + I Y+V+A W L A Sbjct: 69 RSRANTAGAYQKLAPGTHWRWVGR---------MGVLAAFLILSYYSVVAGWTLEYVYEA 119 Query: 123 VTGKILEVDTAQF---FGEAVTGNFVIMPWHIAVIVLTLLTLFAGA-KSIEKTNKIMMPA 178 +T +F F + + + + W + +++T + G K IEK++KIMMP Sbjct: 120 LTNGFTGKTPTEFISSFQQFSSSPWRPVLWLVLFLLVTHFIIVKGVEKGIEKSSKIMMPT 179 Query: 179 FFVLFFILAVRVAFLPGAIEGYKYLFVPDWSYLSNVETWINAMGQAFFSLSITGSGMIVC 238 F++ IL + LPGA G ++L PD+S + +++AMGQAFFSLS+ + Sbjct: 180 LFIIILILVICSVTLPGAGAGIEFLLKPDFSKVDG-NVFLSAMGQAFFSLSLGMGCLCTY 238 Query: 239 GAYLDKKEDIINGALQTGVFDTIAAMIAAFVVIPASFAFGYPASAGPSLMFMTIPEVFKQ 298 +Y K+ ++ A G+ DT A++A F++ PA+F+ G AGPSL+F+T+P VF+Q Sbjct: 239 ASYFSKETNLTKTAFSVGIIDTFVAVLAGFIIFPAAFSVGIQPDAGPSLIFITLPNVFQQ 298 Query: 299 MPFG-----QLLAILFFVSVVFAAISSLQNMFEVVGESIQTRFKMTRKSV-------IVL 346 G + +++F+V + AA++S ++ EVV + F TR + Sbjct: 299 AFSGVPILAYIFSVMFYVLLAMAALTSTISLHEVVTAYLHEEFNFTRGKAARLVTGGCIF 358 Query: 347 LGII-ALVIGI---FIEPENKVGPWMDVVTIYI-IPFGAVLGAISWYWILKKESYMEEL- 400 LGI+ +L +G+ F + D VT I + G + +I W L K+ E+ Sbjct: 359 LGILCSLSLGVMKGFTIFGLGIFDLFDFVTAKIMLTLGGLCISIFTGWYLDKKIVWSEIT 418 Query: 401 NQGS-KVTRSEIYHNVGKYVYVPLVLVVFV--LGVI 433 N GS KV ++ + +Y+ + ++F+ LG+I Sbjct: 419 NDGSLKVPVYKLIIFILRYIAPIAISLIFINELGLI 454 Lambda K H 0.328 0.143 0.434 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 513 Number of extensions: 30 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 438 Length of database: 456 Length adjustment: 33 Effective length of query: 405 Effective length of database: 423 Effective search space: 171315 Effective search space used: 171315 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory